MolNFT v1 · #37947 · protein

Crystal structure of folded and partially unfolded forms of aquifex aeolicus ribosomal protein L20

2GHJ · 50S ribosomal protein L20: “Crystal structure of folded and partially unfolded forms of aquifex aeolicus ribosomal protein L20”. X-ray diffraction, 1 ligand (SO4), 5 pockets (best druggability 0.67). MolNFT v1 #37947 on GenesisL1…

PDB: 2GHJ
Type: protein
Length: 386 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 50S ribosomal protein L20
UniProt: O67086
Ligands: SO4
Pockets: 5 · best druggability 0.67

Structure

x-ray diffraction · 2 distinct chains · 74% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, D	50S ribosomal protein L20	protein	101	73% helix, 0% strand	O67086
B, E	50S ribosomal protein L20	protein	92	74% helix, 0% strand	O67086

Ligands and binding sites

SO4 · Sulfate ion · ion · 6 copies · chains A, E, B, D

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	755	0.67	0.75	72	SO4
2	133	0.45	0.77	23	SO4
3	109	0.42	0.77	21	SO4
4	83	0.30	0.72	17	SO4
5	53	0.30	0.76	10	empty

Interfaces

6 interfaces between chains.

B–E · 1586 Å² buried · 14 hydrogen bonds · protein-protein
A–D · 1460 Å² buried · 15 hydrogen bonds · protein-protein
B–D · 575 Å² buried · 1 hydrogen bond · protein-protein
A–E · 571 Å² buried · 0 hydrogen bonds · protein-protein
A–B · 402 Å² buried · 5 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 modified (engineered).

Compared structures

2GHJ · Crystal structure of folded and partially unfolded forms of Aquifex aeolicus ribosomal… · the same entry in another collection · chain A against A, TM-score 1.00
O67086 · AlphaFold monomer V2.0 prediction for 50S ribosomal protein L20 (O67086) · a predicted model of the same protein · chain A against A, TM-score 0.71

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt O67086
Elsewhere: RCSB PDB 2GHJ · PDBe 2GHJ · UniProt O67086

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